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Mysterious invaders called the Septentriones arrive in Japan and begin attacking the country on a Sunday. To fight back, the heroes in Devil Survivor 2 signed a pact with the devil to become the Thirteen Devil Messengers. The Septentriones show up at least once a day and you have a time limit of seven days to defeat them.

The game starts with the Protagonist and his friend Daichi Shijima finishing a mock exam. Daichi introduces the Protagonist to Nicaea β ver. that allows them to see images of their friends' death, where the player can decide the Protagonist's name and Tico's gender. Daichi remarks that the usual low quality of Nicaea's pictures and videos get it often dismissed as a hoax.

As the two leave the school they come across another schoolmate, Io Nitta, at the subway. Then the three of them get e-mails containing a video that shows one of the trains crashing into the subway station, crushing the three. Almost immediately afterwards, the scene from the video is reenacted before their eyes. However, before the train can crush them, a demon appears and pushes the train out of their way. The group then fights the demons, forming contracts with them. After leaving the destroyed subway station, the trio discover a new application, the Demon Summoning Program, has been installed on their phones with no way to remove it. Makoto Sako appears to interrogate them and asks for their phones. Before she can further question them, they decline and leave. Shortly after, they discover a strange creature which the program identifies as Dubhe. Dubhe swells and causes an explosion, killing the curious civilians investigating it. After seeing its power first-hand, all three scatter from the area when it proceeds to attempt to attack them.

Soon after, the Protagonist and Io receive a death clip from Nicaea showing Daichi's demise at the hands of a powerful demon. They rush to find him still unharmed, but soon after a demon is released from the nearby temple. Makoto then arrives on scene and helps the trio defeat the demons and save Daichi's life. Makoto takes the trio to JP's to treat Io's hurt ankle, where they also meet Yamato Hotsuin, the bureau chief of JP's. They soon overhear that Yamato is going to confine them out of suspicion of abuse of the summoning app and promptly leave.

The group soon meets with Yuzuru Akie (Joe) who ran from the demons that appeared on his phone. After helping Joe defeat the demons and seal his contract, Joe mentions an escape route that they can use and joins the group. Near the escape route, Daichi takes a nearby truck in an attempt to aid the group, but becomes ambushed by Dubhe and drives away. The rest of the group attempts to avoid direct confrontation with Dubhe, and runs toward the exit. However, debris suddenly falls and blocks the path, preventing escape. Just as Dubhe begins to prepare another explosion, Daichi suddenly drives from above and crashes the truck into Dubhe, severely weakening it. The group proceeds to finish off Dubhe, and discovers Daichi hanging on a ledge after jumping out moments prior to sending the truck to Dubhe.

Yamato appears with a few JP's members, and aids the group, stating that all suspicions have been cleared, and that they will provide them with food and shelter for the night. They later learn that Dubhe is one of the Septentriones, a group of alien invaders, which JP's is fighting against.

Prior to bed, Tico will appear, stating that he/she has compiled a brief summary of the day's events, and ask if the protagonist wishes to listen to these events as a recap.

The next day, the Protagonist is awakened by Makoto and informed that Io and Daichi have already left with guards to observe the remains of their home. Yamato asks whether they are finally convinced of the disaster's extent, and offers them the chance to see more by traveling with him to Osaka. The group agrees, and meet up later around a large train. Makoto then activates her cell, which activates the train and causes it to move a few feet further, revealing a hidden passageway. An electric train is revealed at the end, which takes everyone, except Makoto who volunteered to stay behind, to Osaka.

After reaching their destination, the group meets with several other JP's members, as well as Keita Wakui, who was assigned to be their guide. However, Keita ignores his orders and leaves the group shortly after introducing himself. Just then, Nicaea activates, revealing Keita's death at a place with a large flight of stairs. The group agrees to look for Keita and hopefully save him in the process by looking for the place in question.

They soon discover a person who appears to be in a dazed state. As they attempt to reach her, she appears to have summoned demons, deciding that the only way to help her was fight. After knocking her out, another demon appears, and takes her away, leaving the group to deal with the JP's members that appeared shortly after. The group explains what had happened, learning that the girl was hacking into the system, and goes back to searching for Keita.

Shortly after, the group discovers demons chasing after humans, and attempt to stop them. Hinako Kujou appears on the scene and aids them in defeating the demons. She agrees to help the group out in exchange for introducing them to JP's, and reveals the location of the Nicaea clip. If the player reaches the site of his death clip on time, the group aids him in fighting off attacking demons in order to avert the events of his death clip.

After introducing Hinako to Yamato, Yamato shows them that the damage from the disaster has affected the whole country, and even possibly the entire world. The group separates for a bit to reflect on how the destruction has changed their lives, then gathers once again to learn about a new Septentrione that appeared, Merak. They encounter the Septentrione attacking the Tsuutenkaku, and defeat it before it does any further damage. Before leaving Osaka, Daichi volunteers to aid in the retrieval of supplies, and gets off at Nagoya.

After getting out of bed, the Protagonist receives word that communications with the Nagoya branch has been cut off. Fearing for Daichi's safety, he sets off to Nagoya with Io and Joe. There, they meet with Airi Ban and Jungo Torii and discover that riots have broken out over Nagoya, with desperate civilians attacking JP's members and looting supplies.

Not long after discovering the situation, the party receives another death clip from Nicaea. The clip shows Jungo's death at the hands of rioters while Daichi has been taken hostage. Airi suggests that JP's scientist, Fumi Kanno can help search for the location of the death clip.

They soon find Fumi at the base of the radio tower, and the Protagonist's party recognize Fumi from the previous time they saw her hacking the JP's database at the Valgate. However, Botis, the demon controlling her, appears to defend her. The party knocks Fumi out, breaking Botis' mind control over her. They request that Fumi determine the location of the death clip, but her computer is wearing out and requires a new RAM in order for her to search quickly. If the player successfully finds the RAM and delivers it to Fumi, they can arrive in time to avert Jungo's death.

With Daichi rescued, the party turns to the next pressing matter: taking back the Nagoya JP's branch. They arrive at the headquarters, where they find Ronaldo Kuriki leading the riot and looting supplies. Ronaldo is quickly subdued, but shortly after, Phecda attacks, intending to go after the power transformer. Ronaldo grudgingly chooses to cooperate with JP's in defeating Phecda.

After Phecda's defeat, Makoto arrives, and agrees to let Ronaldo go free as thanks for his cooperation in defeating the Septentrione. Before leaving, Ronaldo warns the Protagonist that there is more to JP's than meets the eye, and that the organization is not to be trusted.

Health screenings are ordered for each JP's members to ensure they are in shape to fight. However, before they can go underway, another Septentrione attacks, causing an earthquake in the process. Multiple bodies are reported, and the party is sent to take care of one of them. The Septentrione, while looking similar to a weakened Dubhe, is named Megrez, and the party exterminates it with relative ease.

Following the health screening, another attack from Megrez is detected, but as the party goes to defeat it, a mysterious man appears and destroys the Megrez body while barely lifting a finger. Calling himself the Anguished One, he explains that the presumed bodies of Megrez are merely its buds, and will not cease until the main Megrez body is destroyed. After he leaves, the party deduces that based on his knowledge of demons and the Septentriones, he is the administrator of Nicaea.

Later, the Protagonist receives a request to head to a meeting with Yamato in Osaka. Makoto and the doctor, Otome Yanagiya, meet up with him and prepare to set off using the JP's trains. However, an earthquake from Megrez strikes, trapping the three of them on the platform and preventing the trains from being used. Fumi quickly contacts Makoto and tells them to head for an emergency exit. As a second earthquake also renders that exit inaccessible, Otome requests for Fumi to prepare the Terminal, a mass teleportation device stationed at each JP's branch.

As the Terminals lacked maintenance since Fumi got possessed by Botis, Fumi slightly botches the transportation coordinates, but the three make it safely. After the meeting with Yamato, Fumi successfully repairs the Terminals, allowing the Protagonist to travel freely between Tokyo, Osaka, and Nagoya.

In the middle of the afternoon, the Protagonist receives another death clip, this time indicating Joe's death at the hands of a Pyro Jack while he is escorting citizens out of Centerling Park. Ronaldo is there, but he is unable to help Joe in time. If the player makes the right choices, Joe's death is averted, and the party discovers that he is helpless as he forgot to charge his phone, preventing him from using the summoning app.

Later, Yamato calls the party to headquarters to discuss a means to defeat Megrez. He notes that three Megrez bodies have surfaced and are heading for the towers at Tokyo, Osaka, and Nagoya. The entire party is split into three groups - Tokyo's group comprising of Makoto, Daichi, Io, and Joe, Nagoya's comprising of Fumi, Airi, and Jungo, and Osaka's comprising of Hinako, Keita, and Otome. Each group is set to attack one Megrez body, and all three have to be defeated at the same time, otherwise they will regenerate. The Protagonist gets to pick which group he can join up with.

After Megrez's defeat, Ronaldo calls the Protagonist, indicating that he has some information regarding what Yamato might be hiding. He reveals a photo of a ruined Fukuoka being consumed by some black scar-like void, and asks the Protagonist to get more information regarding the scar.

With news of the photos showing the black scar circulating around the party, the Protagonist asks Fumi to reactivate the Terminal in order to get to Fukuoka. Fumi refuses to do so unless a certain photo of hers is found. After the Protagonist finds her lost photo and ID, they discover that Fumi is under orders not to let anyone go to Fukuoka despite having the Terminal code, and suggests that someone higher in the chain of command be sought out.

Meanwhile, Yamato notes a large number of deaths by neurotoxin across Japan, and suspects another Septentrione to be responsible. He notices that the Septentriones have been attacking the towers across Japan, and reveals to the protagonist that the radio towers are being used as a means to channel the Dragon Stream to project a barrier that protects the cities.

While investigating a park, a large mysterious droplet lands in the park. It explodes after a while, killing the JP's members investigating it. Yamato comes up with a plan to investigate the trajectory of the toxic droplets to determine the location of the Septentrione. After the party escorts him across the map, he locates the next Septentrione - Alioth - which is high up in the sky. He orders for the Tokyo tower to be shut down in order to divert Alioth's attention to another active tower, buying enough time to formulate a plan to attack the Septentrione.

The Protagonist meets the Anguished One again, and he notes that while the demons are unable to hit Alioth at its current altitude, JP's already has a solution at hand. While the Anguished One cannot reveal any more, he hints the Protagonist to "follow the path to Pasupata". The Protagonist asks Makoto about Pasupata, who reveals that it is the burning gaze of Shiva. Kama once shot an arrow at Shiva in an attempt to get him interested in Parvati, but as it interrupted Shiva's meditation, he incinerated Kama in a fit of rage. However, as Kama and Shiva are demons, additional measures are needed to resurrect them - Shiva, being a Lord of Dance, would be interested by an expert dancer, while Kama would require sex appeal to be coaxed out. Hinako willingly volunteers to dance for Shiva, while Airi agrees to act sexy out of her rivalry with Hinako.

The plan would be as follows: After summoning each demon, the myth between Shiva and Kama would be re-enacted. Using Kama as bait, Shiva's Pasupata will hit Alioth and send it crashing down into Sapporo, where its core is vulnerable to attack. While some members object to letting Alioth crash on the city, Yamato soon reveals that the citizens are all dead by then.

After successfully summoning Kama and Shiva, the party pesters Makoto to go to Fukuoka. After revealing that they know of the black scar, Makoto reluctantly accompanies them there. Upon arriving at Fukuoka, Makoto explains that the scar is the Void, which slowly advances upon and consumes any city that is not protected by a barrier. Nothing exists beyond it. Since Makoto cannot elaborate further, the party plans to ask Yamato for more information on the Void.

After leaving Fukuoka, the party receives another death clip - this time of Otome. If the player gets to her in time, they can save Otome by defeating the demons threatening her and the Tsuutenkaku.

With the preparations in place, the myth is re-enacted, with Kama shooting Shiva with his arrow. Yamato then raises Kama high up into the sky where Alioth is, allowing the Pasupata to penetrate both Kama and Alioth. Alioth crashes into Sapporo as planned. Before engaging Alioth's core, Makoto hands the party a neutralizer for them to use on Alioth, as it is speculated that Alioth will utilize some of its own neurotoxin to defend itself. With the neutralizer in tow, the party attacks and defeats Alioth.

Yamato calls the party to a dinner party, where he reveals that the culprit behind the Void and the destruction of the world is Polaris, and the Septentriones are its minions. Yamato also reveals that he intends to create a world where people are rewarded according to their worth - a merit system. Shocked by the revelation, the party is divided over whether to side with Yamato or not.

Later at night, the Protagonist meets with the Anguished One, who elaborates on Polaris' identity: Polaris rules from the Heavenly Throne, and has the ability to intervene with the fates of many universes. The Anguished One states that Yamato can use Polaris' ability to erase the world, modify it, and rebuild it as he wishes. When asked on whether the world can be changed to something different, the Anguished One tells the Protagonist that the path to Polaris will open once all the Septentriones are defeated. However, Polaris will only respond to the will of mankind, rather than just a single person. Daichi leaves to tell the rest of the party of this news.

As the day begins, the party receives word that Ronaldo has declared war on JP's, presumably because he heard of Yamato's declaration to build a merit system. Various individuals now begin showing their opinions between Ronaldo and Yamato.

The Protagonist meets with the Anguished One again, and he explains that Polaris has seen mankind as corrupted and unredeemable, and wishes to destroy the world. The Anguished One wanted to grant mankind their freedom, and so told Yamato of the invasion. If the barrier set up by the Dragon Stream were to prevent the advance of the Void, Polaris would be sure to send the Septentriones to tear it down. Hence the Anguished One set up Nicaea to give humanity the ability to summon demons and the opportunity to stand up to the Septentriones.

Later in the morning, Ronaldo leads the Protagonist to a location that he has discovered underneath the Diet Building. Within that area, they find a large magic circle, used by the Hotsuin family. They guess that this magic circle could be used for a large summoning ritual of sorts.

In the middle of the day, the party encounters Keita struggling against the 6th Septentrione: Mizar. As he attacks its tentacles, it splits apart and forms smaller clones of Mizar. While dealing with the Mizar clones, it escapes, leaving the party to finish off what it left behind.

The party discusses what to do in order to defeat Mizar, as unlike Alioth, demons alone are unable to defeat it. Fumi points out that if that were possible, it would have been tried. The party soon deduces that the Dragon Stream can be used to defeat Mizar, but Yamato notes that the Dragon Stream has been used in conjunction with the radio towers to project a barrier that halts the Void's advance. If the Dragon Stream is channeled to a form to attack Mizar, the rest of Japan will be consumed by the Void within one to three days without the barriers protecting them, but Mizar will destroy what is left of Japan within a day due to its reproduction capability.

The party eventually decides to use the Dragon Stream to vanquish Mizar, but converting the Dragon Stream from its current form is not that simple. The party has to first split into 3 groups and remove the Stakes that seal the Dragon Stream. Following that, a key is needed to channel the Dragon Stream - the demon Lugh. However, due to the Void's advance, Lugh's body is damaged and thus a medium is required. Based on Otome's physical examinations, Io is best suited for channeling Lugh.

Lugh is unsealed at Miyashita Park, but its incomplete form splits its energy into several bits. The strong surge of energy ends up attracting demons to them, and the party needs to regather the pieces of Lugh before the demons take them away. After piecing Lugh together, the party then proceeds to initiate the Dragon Stream's summoning ritual, but not before the Protagonist receives a death clip where Io dies after the Dragon Stream's summoning.

During the ritual, the surge in power not only attracts a number of demons, but the strain from the ritual proves to be taxing on Io's health. With the ritual completed, Io transforms the Dragon Stream into a form to defeat Mizar as a long dragon composed of multiple heads. The Dragon Stream then catches Mizar in its mouth and slams it against a building, attempting to eat it whole. Io floats back down to the ground, and depending on the player's actions prior to the ritual, she may survive, or the strain from channeling Lugh may take her life.

The party ascends to the roof of the building where Mizar is struggling with the Dragon Stream. They notice that Mizar is desperately hanging on to the environment to prevent itself from being eaten, and that there is a limited period of time where the Dragon Stream can remain materialized. The party slowly severs Mizar's tentacles (and the clones it spawns in the process) until it can no longer hold onto the buildings.

The Dragon Stream proceeds to chomp down on Mizar's body. Half of it gets bitten off, and the remaining bit of Mizar attempts to regenerate itself. However, the Dragon Stream pursues and attacks Mizar, with each head in the chain continuing to bite it until Mizar is eaten whole. Remaining Mizar clones leap to the ground in an attempt to escape, only to be crushed by the falling Dragon Stream head. Having fulfilled its purpose, the Dragon Stream head turns to stone.

At 21:00, the Protagonist receives another death clip, showing Makoto being killed by Ronaldo as she fends off another group of rioters. Her death plays out as how the clip shows if the Protagonist sides with Ronaldo in the fight, or takes too long to arrive on scene.

Back at JP's headquarters, Yamato begins to act on his idea of creating a merit system, declaring that he will crush all those who decide to oppose him. Ronaldo, however, appears at the gathering, and declares his intention to create a world of equality - one opposite to Yamato's. Between both of them, Daichi opts for a third choice - a world created without the need to fight his friends. Fumi, Makoto, and Keita side with Yamato. Airi, Otome, and Joe choose to support Ronaldo, while Io, Hinako, and Jungo side with Daichi. The three teams then agree to battle it out the next day, with losing teams being forced to disband.

At the end of the day, the Protagonist is given the option to side with Yamato, Ronaldo, Daichi, or talk with the Anguished One to discuss a fourth path, which will affect the companions available to him from this point onward. Tico also contacts the Protagonist, declaring that Nicaea will shut down from this day onward.

The full title of this day changes depending on who the protagonist has sided with. Daichi's is "Coexistence". Yamato's is "Hierarchy". Ronaldo's is "Equality". The Anguished One's is "Reformation".

As arranged, the Protagonist's party does combat with members of factions which they did not side with. After each battle, the Protagonist can try to convince surviving characters to join his cause. Depending on how high their level of Fate is, they may join him, but Yamato and Ronaldo will not follow if the player has agreed to their opposing cause, or decided to work with the Anguished one, for exception on Daichi's route.

At around 12:00, the Protagonist's party spots the 7th Septentrione: Benetnasch. After trying (and failing) to attack it, Benetnasch demonstrates its Revoke Demons ability, which unsummons all demons, including those held by the party. Realizing that Benetnasch also has the ability "Pacify Humans" to become immune to all attacks by humans (Or those with human form, in The Anguished One's case), the party retreats to discuss a plan to defeat Benetnasch. Fumi notes that Benetnasch negates the summoning program by emitting a signal that interrupts its function.

While rummaging through JP's archives, an entry on Trumpeter is discovered, where its melody has unusual properties. The party then devises a plan to unseal Trumpeter and use its melody to block out Benetnasch's Revoke Demons ability. However, since Trumpeter's waves have a particularly long range, the summoning ability is affected. The party then has to summon their demons before the summoning app is affected by Trumpeter's melody. This way, Benetnasch cannot unsummon their demons, but they cannot summon any additional demons until Benetnasch is defeated.

After Benetnasch's defeat, the party decides to find the path to Polaris, which is said to open once all the Septentriones are defeated. At bedtime, Tico reappears in the Protagonist's phone, explaining that only Nicaea's death clip service has terminated, but the navigators are here to stay. Tico questions the player's plans on using Polaris, before wishing the party the best of luck.

With all seven Septentriones defeated, the party seeks a way to Polaris to change the world. They meet with the Anguished One who, after testing their strength, tells them that Polaris' dimension can be accessed via a Terminal. On the Anguished One's route, the party instead faces Ronaldo and Joe in an attempt to convince them to join their cause. While Joe escapes unharmed, Ronaldo refuses to give up his ideals and is killed by the Anguished One in retaliation.

Despite having defeated the Septentriones, human technology is unable to transport the party to Polaris, let alone modify the Terminal to do that. The Protagonist recalls that the Dragon Stream can potentially accomplish that, and the remnants of it can be found where it was last seen after eating Mizar.

The party finds the Dragon Stream's head still intact at its location. As they ponder over how to transport it to the Terminal, the Dragon awakens from its petrification, demonstrating its ability to eat anything that potentially opposes it. Despite this, the party attacks and defeats the Dragon to calm it down, and it shrinks to a transportable size by the protagonist willing it to do so.

The Dragon Stream is brought to the Terminal, and enhances it such that it is capable of transporting humans to Polaris. However, it cannot be activated yet - the Anguished One reveals himself as Alcor, the final Septentrione that drifted apart from Polaris and his kin. In all routes except for the Anguished One's route, the party defeats and kills him, opening the path to Polaris. On the Anguished One's route, Yamato ambushes them at the enhanced Terminal, where he reveals Alcor's true identity and attacks the party. Refusing to join hands with Alcor, Yamato attempts a last stand but fails, leading him to kill himself by jumping from the terminal.

After Polaris' defeat, whatever happens to the world depends on who the Protagonist has sided with, and what dialogue options the player picked.

A larger selection of demons and races are available, almost guaranteeing that the player always has a competent demon from any race at any point in the game. High-leveled demons even get upgraded versions of Racial Skills.

A wider variety of skills are available, particularly physical skills, to encourage the use of Strength-oriented characters. All skills also only require one stat to be set (compared to 2 stats for some skills in the prequel), allowing them to be usable with more specialized characters.

Unassigned Team leaders still gain a portion of EXP from battles. The Watchful and Vigilant skills can be used to aid leaders which are lagging in level.

The Demon Compendium is introduced to allow players to re-summon their own customized demons.

Add-Ons are introduced as a replacement of Magnetite. These Add-Ons are obtained easily through efficient performance, and grant bonuses during fusion, like increased stats, and the ability to teach a demon any cracked skill of a certain type.

The Titles and rewards system is established. Compendium and unlocked demons are retained in a New Game Plus. Everything else, ranging from retaining demons or macca, removal of EXP limit, bonus bosses, and Compendium discounts have to be purchased using points from achievements.

Slight change in the stat mechanics - Vitality now increases the character's defense against both physical and magical damage, rather than just physical in the previous game, while Magic has merely a minor effect on magic resistance, mostly affecting MP and magic offense, with Strength, much like the previous game, also having a slight effect on physical defense and a more notable effect on physical offense.

The speed stat is undisplayed and roughly constant for all playable characters. As a result, the turn order in battle generally depends solely on actions taken, the number of skirmishes entered before the next turn and order of team leader assignment. Additionally, without using demon skills, each character now has the same movement range of 4.

Currently, Devil Survivor 2 has the most playable characters out of any Shin Megami Tensei game, excluding fusable demons.

Devil Survivor 2 is currently the only game that has a Ultimate Boss fight that involves fighting three bosses at once.

Obtaining different endings will gradually fill out the night sky in the Save Menu's top screen. Seeing the Meritorious, Egalitarian, and Restorer/Liberator endings will fill in the silhouettes of the left, center, and right radio towers, which correspond to Osaka, Nagoya, and Tokyo, respectively. Seeing the Kingmaker ending will add the Big Dipper constellation into the night sky.